• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

亚硫酸氢盐测序数据呈现与汇编（BDPC）网络服务器——一种用于DNA甲基化分析的有用工具。

Bisulfite sequencing Data Presentation and Compilation (BDPC) web server--a useful tool for DNA methylation analysis.

作者信息

Rohde Christian, Zhang Yingying, Jurkowski Tomasz P, Stamerjohanns Heinrich, Reinhardt Richard, Jeltsch Albert

机构信息

School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28725 Bremen, Germany.

出版信息

Nucleic Acids Res. 2008 Mar;36(5):e34. doi: 10.1093/nar/gkn083. Epub 2008 Feb 22.

DOI:10.1093/nar/gkn083
PMID:18296484
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2275153/
Abstract

During bisulfite genomic sequencing projects large amount of data are generated. The Bisulfite sequencing Data Presentation and Compilation (BDPC) web interface (http://biochem.jacobs-university.de/BDPC/) automatically analyzes bisulfite datasets prepared using the BiQ Analyzer. BDPC provides the following output: (i) MS-Excel compatible files compiling for each PCR product (a) the average methylation level, the number of clones analyzed and the percentage of CG sites analyzed (which is an indicator of data quality), (b) the methylation level observed at each CG site and (c) the methylation level of each clone. (ii) A methylation overview table compiling the methylation of all amplicons in all tissues. (iii) Publication grade figures in PNG format showing the methylation pattern for each PCR product embedded in an HMTL file summarizing the methylation data, the DNA sequence and some basic statistics. (iv) A summary file compiling the methylation pattern of different tissues, which is linked to the individual HTML result files, and can be directly used for presentation of the data in the internet. (v) A condensed file, containing all primary data in simplified format for further downstream data analysis and (vi) a custom track file for display of the results in the UCSC genome browser.

摘要

在亚硫酸氢盐基因组测序项目中会产生大量数据。亚硫酸氢盐测序数据呈现与汇编（BDPC）网络界面（http://biochem.jacobs-university.de/BDPC/）会自动分析使用BiQ Analyzer制备的亚硫酸氢盐数据集。BDPC提供以下输出：（i）与MS-Excel兼容的文件，针对每个PCR产物汇编（a）平均甲基化水平、分析的克隆数以及分析的CG位点百分比（这是数据质量的一个指标），（b）在每个CG位点观察到的甲基化水平，以及（c）每个克隆的甲基化水平。（ii）一个甲基化概况表，汇编所有组织中所有扩增子的甲基化情况。（iii）PNG格式的可用于发表的图表，展示每个PCR产物的甲基化模式，该图表嵌入在一个HTML文件中，该文件汇总了甲基化数据、DNA序列和一些基本统计信息。（iv）一个汇总文件，汇编不同组织的甲基化模式，该文件与各个HTML结果文件相关联，可直接用于在互联网上展示数据。（v）一个精简文件，包含所有简化格式的原始数据，用于进一步的下游数据分析；以及（vi）一个自定义轨迹文件，用于在UCSC基因组浏览器中显示结果。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b007/2275153/ca3b5739002f/gkn083f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b007/2275153/31212fdfab82/gkn083f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b007/2275153/34e7ff8a7c89/gkn083f2a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b007/2275153/23e713694e3b/gkn083f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b007/2275153/d549d69f651f/gkn083f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b007/2275153/ca3b5739002f/gkn083f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b007/2275153/31212fdfab82/gkn083f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b007/2275153/34e7ff8a7c89/gkn083f2a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b007/2275153/23e713694e3b/gkn083f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b007/2275153/d549d69f651f/gkn083f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b007/2275153/ca3b5739002f/gkn083f5.jpg

相似文献

1
Bisulfite sequencing Data Presentation and Compilation (BDPC) web server--a useful tool for DNA methylation analysis.亚硫酸氢盐测序数据呈现与汇编（BDPC）网络服务器——一种用于DNA甲基化分析的有用工具。
Nucleic Acids Res. 2008 Mar;36(5):e34. doi: 10.1093/nar/gkn083. Epub 2008 Feb 22.
2
BISMA--fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences.BISMA——用于从独特和重复序列中的单个克隆进行快速准确的亚硫酸氢盐测序数据分析。
BMC Bioinformatics. 2010 May 6;11:230. doi: 10.1186/1471-2105-11-230.
3
New clustering module in BDPC bisulfite sequencing data presentation and compilation web application for DNA methylation analyses.BDPC 亚硫酸氢盐测序数据分析展示和编译网络应用中的新聚类模块，用于 DNA 甲基化分析。
Biotechniques. 2009 Sep;47(3):781-3. doi: 10.2144/000113196.
4
DNA methylation analysis by bisulfite conversion, cloning, and sequencing of individual clones.通过亚硫酸氢盐转化、克隆和单个克隆测序进行DNA甲基化分析。
Methods Mol Biol. 2009;507:177-87. doi: 10.1007/978-1-59745-522-0_14.
5
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.BiQ分析器：亚硫酸氢盐测序DNA甲基化数据的可视化与质量控制
Bioinformatics. 2005 Nov 1;21(21):4067-8. doi: 10.1093/bioinformatics/bti652. Epub 2005 Sep 1.
6
BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data.BSPAT：一种基于高通量亚硫酸氢盐测序数据的用于DNA甲基化共现模式分析的快速在线工具。
BMC Bioinformatics. 2015 Jul 11;16:220. doi: 10.1186/s12859-015-0649-2.
7
methGraph: a genome visualization tool for PCR-based methylation assays.methGraph：一种基于 PCR 的甲基化分析的基因组可视化工具。
Epigenetics. 2010 Feb 16;5(2):159-63. doi: 10.4161/epi.5.2.11161. Epub 2010 Feb 11.
8
QUMA: quantification tool for methylation analysis.QUMA：甲基化分析定量工具
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W170-5. doi: 10.1093/nar/gkn294. Epub 2008 May 16.
9
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing.BiQ Analyzer HT：高通量亚硫酸氢盐测序的 DNA 甲基化位点分析。
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W551-6. doi: 10.1093/nar/gkr312. Epub 2011 May 11.
10
Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.用于离子激流测序仪上靶向扩增子亚硫酸氢盐测序的分析与可视化工具
PLoS One. 2016 Jul 28;11(7):e0160227. doi: 10.1371/journal.pone.0160227. eCollection 2016.

引用本文的文献

1
An MSRE-Assisted Glycerol-Enhanced RPA-CRISPR/Cas12a Method for Methylation Detection.一种用于甲基化检测的MSRE辅助甘油增强型RPA-CRISPR/Cas12a方法
Biosensors (Basel). 2024 Dec 12;14(12):608. doi: 10.3390/bios14120608.
2
27-Hydroxycholesterol, The Estrogen Receptor Modulator, Alters DNA Methylation in Breast Cancer.27-羟胆固醇，一种雌激素受体调节剂，可改变乳腺癌中的 DNA 甲基化。
Front Endocrinol (Lausanne). 2022 Mar 10;13:783823. doi: 10.3389/fendo.2022.783823. eCollection 2022.
3
Locus-specific analysis of DNA methylation patterns in cloned and in vitro fertilized porcine embryos.

本文引用的文献

1
Mechanisms of epigenetic inheritance.表观遗传继承的机制。
Curr Opin Cell Biol. 2007 Jun;19(3):266-72. doi: 10.1016/j.ceb.2007.04.002. Epub 2007 Apr 26.
2
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome.人类基因组中启动子DNA甲基化的分布、沉默潜能及进化影响
Nat Genet. 2007 Apr;39(4):457-66. doi: 10.1038/ng1990. Epub 2007 Mar 4.
3
DNA methylation profiling of human chromosomes 6, 20 and 22.人类6号、20号和22号染色体的DNA甲基化分析
克隆和体外受精猪胚胎中 DNA 甲基化模式的特定位置分析。
J Reprod Dev. 2020 Dec 22;66(6):505-514. doi: 10.1262/jrd.2019-076. Epub 2020 Sep 8.
4
Follistatin treatment modifies DNA methylation of the CDX2 gene in bovine preimplantation embryos.Follistatin 处理可改变牛胚胎植入前 CDX2 基因的 DNA 甲基化。
Mol Reprod Dev. 2020 Sep;87(9):998-1008. doi: 10.1002/mrd.23409. Epub 2020 Aug 10.
5
A novel restriction endonuclease GlaI for rapid and highly sensitive detection of DNA methylation coupled with isothermal exponential amplification reaction.一种用于快速、高灵敏度检测DNA甲基化并结合等温指数扩增反应的新型限制性内切酶GlaI。
Chem Sci. 2017 Dec 11;9(5):1344-1351. doi: 10.1039/c7sc04975g. eCollection 2018 Feb 7.
6
The DNMT3A R882H mutant displays altered flanking sequence preferences.DNMT3A R882H 突变体显示出改变的侧翼序列偏好。
Nucleic Acids Res. 2018 Apr 6;46(6):3130-3139. doi: 10.1093/nar/gky168.
7
Integrating Epigenomics into the Understanding of Biomedical Insight.将表观基因组学融入对生物医学见解的理解中。
Bioinform Biol Insights. 2016 Dec 4;10:267-289. doi: 10.4137/BBI.S38427. eCollection 2016.
8
CD4(+) T cell anergy prevents autoimmunity and generates regulatory T cell precursors.CD4(+) T细胞失能可预防自身免疫并产生调节性T细胞前体。
Nat Immunol. 2016 Mar;17(3):304-14. doi: 10.1038/ni.3331. Epub 2016 Feb 1.
9
A DNMT3A2-HDAC2 Complex Is Essential for Genomic Imprinting and Genome Integrity in Mouse Oocytes.DNMT3A2-HDAC2复合物对小鼠卵母细胞中的基因组印记和基因组完整性至关重要。
Cell Rep. 2015 Nov 24;13(8):1552-60. doi: 10.1016/j.celrep.2015.10.031. Epub 2015 Nov 12.
10
Expression Analysis of Genes Involved in the RB/E2F Pathway in Astrocytic Tumors.星形细胞瘤中RB/E2F信号通路相关基因的表达分析
PLoS One. 2015 Aug 28;10(8):e0137259. doi: 10.1371/journal.pone.0137259. eCollection 2015.
Nat Genet. 2006 Dec;38(12):1378-85. doi: 10.1038/ng1909. Epub 2006 Oct 29.
4
Genomic DNA methylation: the mark and its mediators.基因组DNA甲基化：标记及其介导因子。
Trends Biochem Sci. 2006 Feb;31(2):89-97. doi: 10.1016/j.tibs.2005.12.008. Epub 2006 Jan 5.
5
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.BiQ分析器：亚硫酸氢盐测序DNA甲基化数据的可视化与质量控制
Bioinformatics. 2005 Nov 1;21(21):4067-8. doi: 10.1093/bioinformatics/bti652. Epub 2005 Sep 1.
6
Biochemistry and biology of mammalian DNA methyltransferases.哺乳动物DNA甲基转移酶的生物化学与生物学
Cell Mol Life Sci. 2004 Oct;61(19-20):2571-87. doi: 10.1007/s00018-004-4201-1.
7
The epigenetics of cancer etiology.癌症病因学的表观遗传学
Semin Cancer Biol. 2004 Dec;14(6):427-32. doi: 10.1016/j.semcancer.2004.06.005.
8
Epigenetics in human disease and prospects for epigenetic therapy.人类疾病中的表观遗传学及表观遗传治疗前景。
Nature. 2004 May 27;429(6990):457-63. doi: 10.1038/nature02625.
9
DNA methylation patterns and epigenetic memory.DNA甲基化模式与表观遗传记忆
Genes Dev. 2002 Jan 1;16(1):6-21. doi: 10.1101/gad.947102.
10
Bisulfite genomic sequencing: systematic investigation of critical experimental parameters.亚硫酸氢盐基因组测序：关键实验参数的系统研究
Nucleic Acids Res. 2001 Jul 1;29(13):E65-5. doi: 10.1093/nar/29.13.e65.